메뉴 건너뛰기




Volumn 50, Issue 4, 2003, Pages 537-545

Folding in lipid membranes (FILM): A novel method for the prediction of small membrane protein 3D structures

Author keywords

Fold recognition; Knowledge based; Membrane propensity; Simulated annealing; Transmembrane helix

Indexed keywords

AMYLOID BETA PROTEIN; COAT PROTEIN; GLOBULAR PROTEIN; GLYCOPHORIN A; MEMBRANE PROTEIN; PHOSPHOLAMBAN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE;

EID: 0037339521     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10304     Document Type: Article
Times cited : (42)

References (33)
  • 1
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin E, von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998;7:1029-1038.
    • (1998) Protein Sci , vol.7 , pp. 1029-1038
    • Wallin, E.1    Von Heijne, G.2
  • 2
    • 0032570779 scopus 로고    scopus 로고
    • Do transmembrane superfolds exist?
    • Jones DT. Do transmembrane superfolds exist? FEBS Lett 1998;423:281-285.
    • (1998) FEBS Lett , vol.423 , pp. 281-285
    • Jones, D.T.1
  • 3
    • 0035160589 scopus 로고    scopus 로고
    • Structure determination of membrane-associated proteins from nuclear magnetic resonance data
    • Baleja DJ. Structure determination of membrane-associated proteins from nuclear magnetic resonance data. Anal Biochem 2001;288:1-15.
    • (2001) Anal Biochem , vol.288 , pp. 1-15
    • Baleja, D.J.1
  • 4
    • 0034912255 scopus 로고    scopus 로고
    • Modeling of the structural features of integral-membrane proteins reverse-environment prediction of integral membrane protein structure (REPIMPS)
    • Dastmalchi S, Morris MB, Church WB. Modeling of the structural features of integral-membrane proteins reverse-environment prediction of integral membrane protein structure (REPIMPS). Protein Sci 2001;10:1529-1538.
    • (2001) Protein Sci , vol.10 , pp. 1529-1538
    • Dastmalchi, S.1    Morris, M.B.2    Church, W.B.3
  • 6
    • 0026761782 scopus 로고
    • Modeling of the structure of bacteriorhodopsin. A molecular dynamics study
    • Jähnig F, Edholm O. Modeling of the structure of bacteriorhodopsin. A molecular dynamics study. J Mol Biol 1992;226:837-850.
    • (1992) J Mol Biol , vol.226 , pp. 837-850
    • Jähnig, F.1    Edholm, O.2
  • 7
    • 0016842810 scopus 로고
    • Three-dimensional model of purple membrane obtained by electron microscopy
    • Henderson R, Unwin PNT. Three-dimensional model of purple membrane obtained by electron microscopy. Nature 1975;257:28-32.
    • (1975) Nature , vol.257 , pp. 28-32
    • Henderson, R.1    Unwin, P.N.T.2
  • 8
    • 0027390459 scopus 로고
    • Insertion of peptide chains into lipid membranes: An off-lattice Monte Carlo dynamics model
    • Milik M, Skolnick J. Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins 1993;15:10-25.
    • (1993) Proteins , vol.15 , pp. 10-25
    • Milik, M.1    Skolnick, J.2
  • 9
    • 0024558250 scopus 로고
    • The nature of the hydrophobic binding of small peptides at the bilayer interface: Implications for the insertion of transbilayer helices
    • Jacobs RE, White SH. The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices. Biochemistry 1989;28:3421-3437.
    • (1989) Biochemistry , vol.28 , pp. 3421-3437
    • Jacobs, R.E.1    White, S.H.2
  • 10
    • 0028175436 scopus 로고
    • A method for alpha-helical integral membrane protein fold prediction
    • Taylor WR, Jones DT, Green NM. A method for alpha-helical integral membrane protein fold prediction. Proteins 1994;18:281-294.
    • (1994) Proteins , vol.18 , pp. 281-294
    • Taylor, W.R.1    Jones, D.T.2    Green, N.M.3
  • 11
    • 0031298075 scopus 로고    scopus 로고
    • Successful ab initio prediction of the tertiary structure of NK-Lysin using multiple sequences and recognized supersecondary structural motifs
    • Jones DT. Successful ab initio prediction of the tertiary structure of NK-Lysin using multiple sequences and recognized supersecondary structural motifs. Proteins 1997;1(suppl.):185-191.
    • (1997) Proteins , vol.1 , Issue.SUPPL. , pp. 185-191
    • Jones, D.T.1
  • 12
    • 0035698619 scopus 로고    scopus 로고
    • Predicting novel protein folds using FRAGFOLD
    • Jones DT. Predicting novel protein folds using FRAGFOLD. Proteins 2001;45(suppl 5):127-132.
    • (2001) Proteins , vol.45 , Issue.SUPPL. 5 , pp. 127-132
    • Jones, D.T.1
  • 13
    • 0031008715 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database: Its relevance to human molecular medical research
    • Bairoch A, Apweiler R. The SWISS-PROT protein sequence database: its relevance to human molecular medical research. J Mol Med 1997;75:312-316.
    • (1997) J Mol Med , vol.75 , pp. 312-316
    • Bairoch, A.1    Apweiler, R.2
  • 16
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 17
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones DT. GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999;287:797-815.
    • (1999) J Mol Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 19
    • 0029831680 scopus 로고    scopus 로고
    • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
    • Kelley LA, Gardner SP, Sutcliffe MJ. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Eng 1996;9:1063-1065.
    • (1996) Protein Eng , vol.9 , pp. 1063-1065
    • Kelley, L.A.1    Gardner, S.P.2    Sutcliffe, M.J.3
  • 20
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin LJ, Bryson K, Jones, DT. The PSIPRED protein structure prediction server. Bioinformatics 2000;16:404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 21
    • 0032570779 scopus 로고    scopus 로고
    • Do transmembrane protein superfolds exist?
    • Jones DT. Do transmembrane protein superfolds exist? FEBS Lett 1998;423:281-285.
    • (1998) FEBS Lett , vol.423 , pp. 281-285
    • Jones, D.T.1
  • 22
    • 0028211273 scopus 로고
    • A model recognition approach to the predication of all-helical membrane protein structure and topology
    • Jones DT, Taylor WR, Thornton JM. A model recognition approach to the predication of all-helical membrane protein structure and topology. Biochemistry 1994;33:3038-3049.
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 23
    • 0026557830 scopus 로고
    • The functions of tryptophan residues in membrane proteins
    • Schiffer M, Chang CH, Stevens FJ. The functions of tryptophan residues in membrane proteins. Protein Eng 1992;5:213-214.
    • (1992) Protein Eng , vol.5 , pp. 213-214
    • Schiffer, M.1    Chang, C.H.2    Stevens, F.J.3
  • 24
    • 0032552880 scopus 로고    scopus 로고
    • The preference of tryptophan for membrane interfaces
    • Yau WM, Wimley WC, Gawrisch K, White SH. The preference of tryptophan for membrane interfaces. Biochemistry 1998;37:14713-14718.
    • (1998) Biochemistry , vol.37 , pp. 14713-14718
    • Yau, W.M.1    Wimley, W.C.2    Gawrisch, K.3    White, S.H.4
  • 25
    • 0030983047 scopus 로고    scopus 로고
    • Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria
    • Wallin E, Tsukihara T, Yoshikawa S, von Heijne G, Elofsson A. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci 1997;6:808-815.
    • (1997) Protein Sci , vol.6 , pp. 808-815
    • Wallin, E.1    Tsukihara, T.2    Yoshikawa, S.3    Von Heijne, G.4    Elofsson, A.5
  • 26
    • 0031740601 scopus 로고    scopus 로고
    • Hydrophobic interactions of peptides with membrane interfaces
    • White SH, Wimley WC. Hydrophobic interactions of peptides with membrane interfaces. Biochim Biophys Acta 1998;1376:339-352.
    • (1998) Biochim Biophys Acta , vol.1376 , pp. 339-352
    • White, S.H.1    Wimley, W.C.2
  • 27
    • 0033597281 scopus 로고    scopus 로고
    • A turn propensity scale for transmembrane helices
    • Monne M, Hermasson M, von Heijne G. A turn propensity scale for transmembrane helices. J Mol Biol 1999;288:141-145.
    • (1999) J Mol Biol , vol.288 , pp. 141-145
    • Monne, M.1    Hermasson, M.2    Von Heijne, G.3
  • 28
    • 0034703270 scopus 로고    scopus 로고
    • Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: Molecular dynamics calculations
    • Petrache HI, Grossfield A, MacKenzie KR, Engelman DM, Woolf TB. Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations. J Mol Biol 2000;302:727-746.
    • (2000) J Mol Biol , vol.302 , pp. 727-746
    • Petrache, H.I.1    Grossfield, A.2    MacKenzie, K.R.3    Engelman, D.M.4    Woolf, T.B.5
  • 30
    • 0031577283 scopus 로고    scopus 로고
    • FD coat protein structure in membrane environments: Structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix
    • Almeida FC, Opella SJ. FD coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix. J Mol Biol 1997;270:481-495.
    • (1997) J Mol Biol , vol.270 , pp. 481-495
    • Almeida, F.C.1    Opella, S.J.2
  • 31
    • 0032483035 scopus 로고    scopus 로고
    • Solution structure of amyloid beta-peptide(1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is?
    • Coles M, Bicknell W, Watson AA, Fairlie DP, Craik DJ. Solution structure of amyloid beta-peptide(1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is? Biochemistry 1998;37:11064-11077.
    • (1998) Biochemistry , vol.37 , pp. 11064-11077
    • Coles, M.1    Bicknell, W.2    Watson, A.A.3    Fairlie, D.P.4    Craik, D.J.5
  • 32
    • 0035834520 scopus 로고    scopus 로고
    • Helical structure of phospholamban in membrane bilayers
    • Smith SO, Kawakami T, Liu W, Ziliox M, Aimoto S. Helical structure of phospholamban in membrane bilayers. J Mol Biol 2001;313:1139-1148.
    • (2001) J Mol Biol , vol.313 , pp. 1139-1148
    • Smith, S.O.1    Kawakami, T.2    Liu, W.3    Ziliox, M.4    Aimoto, S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.